Marine and Freshwater Research Marine and Freshwater Research Society
Advances in the aquatic sciences

Mitochondrial DNA reveals phylogenetic structuring and cryptic diversity in Australian freshwater macroinvertebrate assemblages

Andrew M. Baker A C , Jane M. Hughes A , John C. Dean B and Stuart E. Bunn A

A Cooperative Research Centre for Freshwater Ecology, Centre for Riverine Landscapes, Griffith University, Nathan Campus, Qld 4111, Australia.

B Environment Protection Authority, Freshwater Sciences Unit, Ernest Jones Drive, Macleod, Vic. 3085, Australia.

C Corresponding author. Email:

Marine and Freshwater Research 55(6) 629-640
Submitted: 12 March 2004  Accepted: 7 June 2004   Published: 14 September 2004


Freshwater catchments of south-east Australia possess generally rich and diverse macroinvertebrate faunas, although the genetic structuring of these assemblages is poorly known. In this study, we assessed mitochondrial phylogenetic structure within four genera of macroinvertebrates from the Sydney Water Supply Catchment, south-east Australia: Euastacus (parastacid crayfish), Cheumatopsyche (hydropsychid caddisflies), Atalophlebia (leptophlebiid mayflies) and Paratya (atyid shrimp), with a view to prioritising areas of high diversity for future conservation efforts. We found extremely divergent (≈4–19%) cytochrome c oxidase subunit I (COI) lineages within all surveyed groups, many of which corresponded to recognised taxa, although there was also evidence of cryptic species within three genera; Euastacus, Atalophlebia and Paratya. Distributions of these three genera were associated with high altitude streams, above dam impoundments. Our results have important implications for management of the Sydney Water Supply Catchment. Future disturbance in this region is likely to be high and priority should be directed towards preserving the diversity of fauna in these upland areas. This comparative phylogenetic approach may have value as a means to focus and direct conservation efforts in other areas supporting high biodiversity.

Extra keywords: Atalophlebia, Cheumatopsyche, cryptic diversity, Euastacus, mitochondrial DNA, Paratya, phylogenetic.


Avise J. C. 1994 ‘Molecular Markers, Natural History and Evolution.’ Chapman and Hall New York, USA.

Baker A. M. Hurwood D. A. Krogh M. Hughes J. M. in press Mitochondrial DNA signatures of restricted gene flow within divergent lineages of an atyid shrimp (Paratya australiensis). Heredity

Baker A. M. Williams S. A. Hughes J. M. 2003 Patterns of spatial genetic structuring in a hydropsychid caddisfly (Cheumatopsyche sp. AV1) from southeastern Australia. Molecular Ecology 12 3313 3324

Barker G. M. 2002 Phylogenetic diversity: a quantitative framework for measurement of priority and achievement in biodiversity conservation. Biological Journal of the Linnean Society 76 165 194 doi:10.1046/J.1095-8312.2002.00055.X

Bininda-Emonds O. R. P. Vazquez D. Manne L. L. 2000 The calculus of biodiversity: integrating phylogeny and conservation. Trends in Ecology & Evolution 15 92 94 doi:10.1016/S0169-5347(99)01781-4

Boyero L. 2002 Insect biodiversity in freshwater ecosystems: is there any latitudinal gradient? Marine and Freshwater Research 53 753 755 doi:10.1071/MF01232

Bunn S. E. Davies P. M. 1990 Why is the stream fauna of south-western Australia so impoverished. Hydrobiologia 194 169

Chenoweth S. F. Hughes J. M. 2003 Speciation and phylogeography in Caridina indistincta, a complex of freshwater shrimps from Australian heathland streams. Marine and Freshwater Research 54 807 812

Chessman B. C. Williams S. A. 1999 Biodiversity and conservation of river macroinvertebrates on an expanding urban fringe: western Sydney, New South Wales, Australia. Pacific Conservation Biology 5 36 55

Dean J. C. 1999a ‘Preliminary Keys for the Identification of Australian Trichoptera Larvae of the Family Hydropsychidae.’ Cooperative Research Centre for Freshwater Ecology Albury, Australia.

Dean J. C. 1999b ‘Preliminary Keys for the Identification of Australian Mayfly Nymphs of the Family Leptophlebiidae.’ Cooperative Research Centre for Freshwater Ecology Albury, Australia.

Doyle J. J. Doyle J. L. 1987 A rapid DNA isolation procedure for small quantities of leaf tissue. Phytochemistry Bulletin 19 11 15

Eck R. V. Dayhoff M. O. 1966 ‘Atlas of Protein Sequence and Structure 1966.’ National Biomedical Research Foundation Silver Spring, MD, USA.

Faith D. P. 1992 Conservation evaluation and phylogenetic diversity. Biological Conservation 61 1 10

Faith D. P. 2002 Quantifying biodiversity: a phylogenetic perspective. Conservation Biology 16 248 252 doi:10.1046/J.1523-1739.2002.00503.X

Faith D. P. Reid C. A. M. Hunter J. 2004 Integrating phylogenetic diversity, complementarity, and endemism for conservation assessment. Conservation Biology 18 255 261

Felsenstein J. 1993 PHYLIP – Phylogeny Inference Package (Version 3.2). Cladistics 5 164 166

Felsenstein J. Churchill G. A. 1996 A hidden Markov model approach to variation among sites in rate of evolution. Molecular Biology and Evolution 13 93 104

Feral J. P. 2002 How useful are the genetic markers in attempts to understand and manage marine biodiversity. Journal of Experimental Marine Biology and Ecology 268 121 145

Folmer O. Black M. Hoeh W. Lutz R. Vrijenhoek R. 1994 DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3 294 299

Growns I. O. Growns J. E. 2001 Ecological effects of flow regulation on macroinvertebrate and periphytic diatom assemblages in the Hawkesbury-Nepean River, Australia. Regulated Rivers Research Management 17 275 293

Hall T. A. 1999 BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41 95 98

Horwitz P. 1995 ‘A Preliminary Key to the Species of Decapoda (Crustacea: Malacostraca) Found in Australian Inland Waters.’ Cooperative Research Centre for Freshwater Ecology Albury, Australia.

Huelsenbeck J. P. Ronquist F. 2001 MRBAYES: Bayesian inference of phylogenetic trees. Biometrics 17 754 755

Kumar S. Tamura T. Jakobsen I. B. Nei M. 2001 MEGA2: molecular evolutionary genetics analysis software. Bioinformatics (Oxford, England) 17 1244 1245 doi:10.1093/BIOINFORMATICS/17.12.1244

Lake P. S. Barmuta L. A. Boulton A. J. Campbell I. C. StClair R. M. 1985 Australian streams and Northern Hemisphere: comparisons and problems. Proceedings of the Ecological Society of Australia 14 61 82

Lee M. S. Y. 2003 Species concepts and species reality: salvaging a Linnaean rank. Journal of Evolutionary Biology 16 179 188

Meegaskumbura M. Bossuyt F. Pethiyagoda R. Manamendra-Arachchi K. Bahir M. Milinkovitch M. C. Schneider C. J. 2002 Sri Lanka: an amphibian hotspot. Science 298 379 doi:10.1126/SCIENCE.298.5592.379

Merrick J. R. 1993 ‘Freshwater Crayfishes of New South Wales.’ Linnean Society of New South Wales Milson’s Point, New South Wales, USA.

Mishler B. Brandon R. N. 1987 Individuality, pluralism and the phylogenetic species concept. Biology and Philosophy 2 397 414

Mishler B. Theriot E. C. 2000 The phylogenetic species concept: monophyly, apomorphy and phylogenetic species concepts. ‘Species Concepts and Phylogenetic Theory: a Debate’. D.Wheeler Q. Meier R. 44 54 Columbia University Press New York, USA.

Morgan G. J. 1997 Freshwater crayfish of the genus Euastacus Clark (Decapoda: Parastacidae) from New South Wales, with a key to all species of the genus. Records of the Australian Museum Supplement 23 1 110

Moritz C. Faith D. P. 1998 Comparative phylogeography and the identification of genetically divergent areas for conservation. Molecular Ecology 7 419 429

Palumbi S. R. Martin A. Romano S. McMillan W. O. Stice L. Grabowski G. 1991 ‘The Simple Fools Guide PCR.’ Kewalo Marine Laboratory University of Hawaii

Posada D. Crandall K. A. 1998 Modeltest: testing the model of DNA substitution. Bioinformatics (Oxford, England) 14 817 818

de Queiroz K. Donoghue M. J. 1988 Phylogenetic systematics and the species problem. Cladistics 4 317 338

Rannala B. Yang Z. H. 1996 Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. Journal of Molecular Evolution 43 304 311

Recher H. F. Hutchings P. A. Rosen S. 1993 The biota of the Hawkesbury-Nepean catchment: reconstruction and restoration. Australian Journal of Zoology 29 3 41

Saitou N. Nei M. 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4 406 425

Sechrest W. Brooks T. M. da Fonseca G. A. B. Konstant W. R. Mittermeier R. A. Purvis A. Rylands A. B. Gittleman J. L. 2002 Hotspots and the conservation of evolutionary diversity. Proceedings of the National Academy of Sciences of the United States of America 99 2067 2071

Swofford D. L. 2001 ‘PAUP* Phylogenetic Analysis Using Parsimony (*and Other Methods) Version 4.’ Sinauer Associates Sunderland, MA, USA.

Sydney Catchment Authority 2002 ‘Draft Bulk Water Network Delivery Plan.’ Bulk Water Division Sydney, Australia

Williams W. D. 1977 Some aspects of the ecology of Paratya australiensis (Crustacea: Decapoda: Atyidae). Australian Journal of Marine and Freshwater Research 28 403 415

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